Current COVID-19 pandemic and previous SARS/MERS outbreaks have caused a series of major crises to global public health. We must integrate the large and exponentially growing amount of heterogeneous coronavirus data to better understand coronaviruses and associated disease mechanisms, in the interest of developing effective and safe vaccines and drugs. Ontologies have emerged to play an important role in standard knowledge and data representation, integration, sharing, and analysis. We have initiated the development of the community-based Coronavirus Infectious Disease Ontology (CIDO). (...) As an Open Biomedical Ontology (OBO) library ontology, CIDO is an open source and interoperable with other existing OBO ontologies. In this article, the general architecture and the design patterns of the CIDO are introduced, CIDO representation of coronaviruses, phenotypes, anti-coronavirus drugs and medical devices (e.g. ventilators) are illustrated, and an application of CIDO implemented to identify repurposable drug candidates for effective and safe COVID-19 treatment is presented. (shrink)

The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the (...) development of the community-based Coronavirus Infectious Disease Ontology in early 2020. -/- As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein terms from the Protein Ontology, COVID-19-related phenotype terms from the Human Phenotype Ontology, and over 100 COVID-19 terms for vaccines (both authorized and in clinical trial) from the Vaccine Ontology. CIDO systematically represents variants of SARS-CoV-2 viruses and over 300 amino acid substitutions therein, along with over 300 diagnostic kits and methods. CIDO also describes hundreds of host-coronavirus protein-protein interactions (PPIs) and the drugs that target proteins in these PPIs. CIDO has been used to model COVID-19 related phenomena in areas such as epidemiology. The scope of CIDO was evaluated by visual analysis supported by a summarization network method. CIDO has been used in various applications such as term standardization, inference, natural language processing (NLP) and clinical data integration. We have applied the amino acid variant knowledge present in CIDO to analyze differences between SARS-CoV-2 Delta and Omicron variants. CIDO's integrative host-coronavirus PPIs and drug-target knowledge has also been used to support drug repurposing for COVID-19 treatment. -/- CIDO represents entities and relations in the domain of coronavirus diseases with a special focus on COVID-19. It supports shared knowledge representation, data and metadata standardization and integration, and has been used in a range of applications. (shrink)

The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD as a post-translational modification (...) reference. We illustrate its use in facilitating an alignment between PRO and Reactome protein entities. We also address issues of scalability, describing our first steps into the use of text mining to identify protein-related entities, the large-scale import of proteoform information from expert curated resources, and our ability to dynamically generate PRO terms. Web views for individual terms are now more informative about closely-related terms, including for example an interactive multiple sequence alignment. Finally, we describe recent improvement in semantic utility, with PRO now represented in OWL and as a SPARQL endpoint. These developments will further support the anticipated growth of PRO and facilitate discoverability of and allow aggregation of data relating to protein entities. (shrink)

To reject skepticism and lay the foundation for the certainty of knowledge, Kant raised the question of how synthetic a priori proposition is possible. In his solution, the new content of knowledge comes from the syntheses of experience a posteriori, and the universal necessity of knowledge is guaranteed by it’s a priority. Under the influence of Kant, the concept of a priori and necessity has long been regarded as coextensive. But Saul Kripke believes that this will confuse different philosophical fields: (...) a priori is an epistemological concept, which involves the way or means of acquiring knowledge, and necessity is a metaphysical concept, which involves the possible ways or states of the world. The key point is that, on Kripke, there is no necessary connection between these two fields. He raised some famous examples of the necessary a posteriori. More remarkably, in his explanation of necessary a posteriori, although he did not clearly propose the distinction between epistemic possibility and metaphysical possibility, he had laid the foundation for this distinction. Furthermore, on Manuel Garcia-Carpintero and Josep Macia, when Kripke talks about necessary a posteriori by appealing to two relevant expressions, what he proposed can be taken as kind of ‘blueprint for 2-D accounts’. (Manuel Garcia-Carpintero and Josep Macia, 2006, p.2) There are different forms of two-dimensionalism in semantics. I will focus on David Chalmers’s epistemic version and Scott Soames’ criticism. With the framework of possible world semantics established by Kripke and others, David Chalmers’ epistemic two-dimensionalism deals with the relationship between epistemic and metaphysical modalities from a quite different perspective, and then gives an elegant definition to necessary a posteriori and other modal concepts. Scott Soames criticized two-dimensionalism based on Kripke's modal realism and essentialism, and developed Kripke's account of necessary a posteriori. But according to Chalmers, Soames also uses a two-dimensional system himself to analyze cases of the necessary a posteriori. In the first two part of this paper I will briefly introduce the epistemic two-dimensionalism and specify the similarities between Kripke-Soames and Chalmers when they interpret necessary a posteriori. In the third part I turn to their difference by the analysis of relationship between epistemic possibility and metaphysical possibility which is the key issue for illuminating necessary a posteriori. (shrink)